Package Bio :: Package expressions :: Module hmmpfam
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Module hmmpfam

source code

Martel expression for the hmmpfam database search program in hmmer.

This has been tested with version 2.2g. I should also make it work with 2.1.1 output.

XXX This isn't completely finished and doesn't do everything quite right. The main two problems being that it isn't well tested for a wide variety of outputs and that the family line is not parsed into it's respective parts (see multitude of comments on this below).

Variables [hide private]
  program_description = Std.application_name(Str("hmmpfam"))+ To...
  program_version = Str("HMMER ")+ Std.application_version(Re(r"...
  copyright = ToEol()+ ToEol()
  files = ToEol()+ Str("HMM file:")+ Spaces()+ Std.database_name...
  header = Std.search_header(program_description+ program_versio...
  sequence_info = ToEol()+ Str("Query sequence:")+ Spaces()+ Gro...
  model_name = Re(r"[\w-]+")
  family_header = ToEol()+ Str("Scores")+ ToEol()+ Str("Model")+...
  no_hit_line = Spaces()+ Str("[no hits above thresholds]")+ Any...
  family_hit_line = Group("family_model", model_name)+ Spaces()+...
  domain_header = ToEol()+ Str("Parsed for domains:")+ AnyEol()+...
  symbol_forward = Str(".") | Str("[")
  symbol_reverse = Str(".") | Str("]")
  match_symbols = symbol_forward+ symbol_reverse
  domain_hit_line = Group("domain_model", model_name)+ Spaces()+...
  alignment_header = ToEol()+ Str("Alignments of top-scoring dom...
  domain_align_header = Group("dalign_name", model_name)+ Str(":...
  rf_line = Spaces()+ Str("RF ")+ ToEol()
  domain_align_top = Spaces()+ UntilEol("dalign_match_top")+ Any...
  domain_align_middle = Spaces()+ UntilEol("dalign_match_middle"...
  domain_align_bottom = Spaces()+ ToSep("dalign_query_name", " "...
  domain_alignment = domain_align_header+ Rep1(Opt(rf_line)+ dom...
  record_end = Str("//")+ AnyEol()
  record = Std.record(Rep(sequence_info+ family_header+(no_hit_l...
  format = HeaderFooter("hmmpfam", {}, header, RecordReader.Coun...
  __warningregistry__ = {('Bio.expressions was deprecated, as it...
Variables Details [hide private]

program_description

Value:
Std.application_name(Str("hmmpfam"))+ ToEol()

program_version

Value:
Str("HMMER ")+ Std.application_version(Re(r"\d\.\d\w") | Re(r"\d\.\d\.\
\d"))+ ToEol()

files

Value:
ToEol()+ Str("HMM file:")+ Spaces()+ Std.database_name(UntilEol())+ An\
yEol()+ Str("Sequence file:")+ Spaces()+ Group("inputfile_name", Until\
Eol())+ AnyEol()+ ToEol()

header

Value:
Std.search_header(program_description+ program_version+ copyright+ fil\
es)

sequence_info

Value:
ToEol()+ Str("Query sequence:")+ Spaces()+ Group("query_name", UntilEo\
l())+ AnyEol()+ Str("Accession:")+ Spaces()+ Group("query_accession", \
UntilEol())+ AnyEol()+ Str("Description:")+ Spaces()+ Std.query_descri\
ption(UntilEol())+ AnyEol()

family_header

Value:
ToEol()+ Str("Scores")+ ToEol()+ Str("Model")+ ToEol()+ Str("-----")+ \
ToEol()

no_hit_line

Value:
Spaces()+ Str("[no hits above thresholds]")+ AnyEol()

family_hit_line

Value:
Group("family_model", model_name)+ Spaces()+ ToEol("family_information\
")

domain_header

Value:
ToEol()+ Str("Parsed for domains:")+ AnyEol()+ Str("Model")+ ToEol()+ \
Str("-----")+ ToEol()

domain_hit_line

Value:
Group("domain_model", model_name)+ Spaces()+ Group("domain_domain", In\
teger()+ Str("/")+ Integer())+ Spaces()+ Integer("domain_seq-f")+ Spac\
es()+ Integer("domain_seq-r")+ Spaces()+ Group("domain_seq_symbols", m\
atch_symbols)+ Spaces()+ Integer("domain_hmm-f")+ Spaces()+ Integer("d\
omain_hmm-t")+ Spaces()+ Group("domain_hmm_symbols", match_symbols)+ S\
paces()+ Float("domain_score")+ Spaces()+ Float("domain_evalue")+ AnyE\
ol()

alignment_header

Value:
ToEol()+ Str("Alignments of top-scoring domains:")+ AnyEol()

domain_align_header

Value:
Group("dalign_name", model_name)+ Str(": domain ")+ Integer("dalign_of\
_domain")+ Str(" of ")+ Integer("dalign_total_domain")+ Str(", from ")\
+ Integer("dalign_domain_start")+ Str(" to ")+ Integer("dalign_domain_\
end")+ Str(": score ")+ Float("dalign_score")+ Str(", E = ")+ Float("d\
align_evalue")+ AnyEol()

domain_align_top

Value:
Spaces()+ UntilEol("dalign_match_top")+ AnyEol()

domain_align_middle

Value:
Spaces()+ UntilEol("dalign_match_middle")+ AnyEol()

domain_align_bottom

Value:
Spaces()+ ToSep("dalign_query_name", " ")+ Spaces()+ Alt(Integer("dali\
gn_query_start")+ Spaces()+ Group("dalign_match_bottom", Re("[\w\-]+")\
)+ Spaces()+ Integer("dalign_query_end")+ Spaces()+ AnyEol(), Str("- "\
)+ ToEol())+ ToEol()

domain_alignment

Value:
domain_align_header+ Rep1(Opt(rf_line)+ domain_align_top+ domain_align\
_middle+ domain_align_bottom)

record

Value:
Std.record(Rep(sequence_info+ family_header+(no_hit_line | Rep1(family\
_hit_line))+ domain_header+(no_hit_line | Rep1(domain_hit_line))+ alig\
nment_header+(no_hit_line | Rep1(domain_alignment))+ record_end))

format

Value:
HeaderFooter("hmmpfam", {}, header, RecordReader.CountLines, (8,), rec\
ord, RecordReader.EndsWith, ("//\n",), None, None, None)

__warningregistry__

Value:
{('Bio.expressions was deprecated, as it does not work with recent ver\
sions of mxTextTools. If you want to continue to use this module, plea\
se get in contact with the Biopython developers at biopython-dev@biopy\
thon.org to avoid permanent removal of this module from Biopython',
  <type 'exceptions.DeprecationWarning'>,
  13): 1}